The Microsoft Research Connections blog shares stories of collaborations with computer scientists at academic and scientific institutions to advance technical innovations in computing, as well as related events, scholarships, and fellowships.

The Jim Gray eScience Award—named for Jim Gray, a Technical Fellow at Microsoft Research and a Turing Award winner who disappeared at sea in 2007—recognizes innovators whose work makes science easier for other scientists.

It was a special pleasure to be part of the audience in Stockholm as Tony Hey, corporate vice president of Microsoft Research Connections, presented the 2011 award to Mark Abbott at the Microsoft Research eScience in Action Workshop. Mark Abbott is dean and professor in the College of Oceanic and Atmospheric Sciences at Oregon State University. He is also serving a six-year term on the National Science Board, which oversees the National Science Foundation and provides scientific advice to the White House and to Congress. I was very proud to be part of the eScience research community as we applauded Mark for his career-long contributions to integrating biological and physical science, making early innovations in data-intensive science, and providing educational leadership.

After the applause, the audience learned that another award recipient was to be announced. Technically, the Jim Gray eScience Award was started in 2007, but the first award was presented in 2008. However, the 2007 award ceremony was put on hold due to Jim’s disappearance. That year, Tony Hey publically recognized Alex Szalay, a professor in the Department of Physics and Astronomy at John Hopkins University, for his foundational contributions to interdisciplinary advances in the field of astronomy and groundbreaking work with Jim Gray, but did not present him with an award. Now after four years, Tony Hey was able to call Alex to the stage and formally present him with the 2007 Jim Gray eScience Award. This began a great evening as we sat back to enjoy Mark Abbott’s view on how “data-intensive science is more than just speeds and feeds.”

Please join me in paying tribute to these two outstanding researchers who have advanced Jim Gray’s vision of data-intensive science.

The first documented case of HIV was in 1981. Today, HIV is viewed as a treatable, chronic disease by many in developed nations where treatments are readily available. Yet HIV continues to devastate, claiming the lives of 1.8 million people annually—about 5,000 deaths per day. Those fortunate enough to have access to treatment must arrange their lives around a strict treatment regime that can overshadow everyday activities. On this World AIDS Day, we are taking time to focus on this global crisis, and to remember that the battle is not over. We would also like to shine a light on a possible weapon in the battle to stop the virus: an HIV vaccine.

HIV remains a threat throughout the world. It has been particularly devastating in the sub-Saharan region of Africa, where two-thirds of the population is HIV positive by age 25. The occurrence of HIV is higher for women than men; an estimated one in three women seeking care during pregnancy is HIV positive. By age 35, the infection rate for men rivals that of women in the region.

The South African government offers free antiretroviral (AVR) therapy for HIV-positive residents. The precision timing required by AVR therapy is a dominant factor in the life of any HIV-positive individual. For Purity, a 30-year-old resident of the KwaZulu-Natal province in South Africa, it is a constant struggle. “Early in the morning at 8:00, I take Tenofovir and Lamivudine. After I eat my breakfast, I take Bactrim and vitamins. In the evening, at 8:00, I take Stocrin and Lamivudine.”

Purity does not know exactly when she contracted HIV. She knew she was ill, and sought treatment at the hospital. She was diagnosed with tuberculosis and then soon after, HIV. “I thought my life was over,” she remembers. “People told us that if you are HIV positive, you’re dead—you’re not going to live. But there is always hope. There is always a way. And I’m here today. I’m fine.”

Purity hopes for a cure for those who already have HIV. She also hopes that a vaccine will be developed to prevent others from contracting HIV and suffering the physical, mental, and emotional pain that HIV has inflicted upon her life. Until that time, she has a message of hope for those who contract the virus.

“If I met somebody [who was] HIV positive, I would tell them to hold on. They are still alive. There’s hope,” she said. “They must dream, because that’s what keeps me going. Dreams—dreams and hopes. Because if you don’t have hope and dreams, you see yourself as good as dead.”

The Search for a Vaccine

Researchers are working hard to make Purity’s dream of a cure—or at least a vaccine—come true. A number of HIV vaccines are in various stages of development. A notable HIV vaccine effort is being led by Bruce Walker, director of the Ragon Institute at Massachusetts General Hospital, MIT and Harvard, and a professor of medicine at the University of KwaZulu-Natal. Walker is leading a multi-organizational effort to test a vaccine in Durban, South Africa—the epicenter of the African HIV epidemic. Joining Walker and the Ragon Institute are the Centre for the AIDS Programme of Research in South Africa (CAPRISA) and the KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH). Microsoft Research is working with the Ragon Institute to quantify how the immune system attacks various fragments of HIV—data that we hope will, one day, lead to a vaccine or possibly even a cure.

Understanding HIV

One of the biggest challenges we face in building a vaccine for HIV is that HIV mutates a lot. How much? Well, consider this: if you look at all the mutations that have ever occurred in the influenza virus—the virus that causes the flu—you’ll see about the same amount of mutation of HIV in a single individual who has contracted the virus. You’ve heard how difficult it has been to develop an effective flu vaccine. Imagine how difficult it is to create a vaccine for HIV.

Difficult does not mean impossible, however. While HIV does have a strong evolutionary advantage—its ability to mutate—we believe it also has an “Achilles heel.” There are certain fragments of HIV that, we believe, when attacked by our immune system, will become sick and die. We are cataloguing those fragments of HIV that we know are vulnerable to attacks by the immune system. Once that is done, we plan to develop a vaccine that will train our immune systems to attack just those fragments of HIV, and ignore all the other parts of the virus that are not vulnerable.

To catalog the vulnerable fragments of HIV, we’re taking data from many individuals in South Africa and correlating that data with how the patient’s body is reacting to the virus. Is it controlling HIV? Or is the virus continuing to copy itself and survive? We’re also sorting through the different mutations of HIV to identify when and where the immune system attacks, and how HIV mutates in response.

It’s an incredibly daunting task: there are millions of possible combinations to sort through. It would take years to process the volume of data we receive on a single computer. Therefore, we’re committing thousands of machines to this task, using an algorithm we developed at Microsoft Research called PhyloD. Combined, our hardware and software can complete the analysis in just hours—a critical advantage in the fight against HIV. We send the information back to Ragon in Africa and we then work together to identify follow-up experiments. In addition to our targeted research, we have also made some general discoveries that are applicable to all immune system research—not just HIV.

Fighting More Than Just HIV

We are continuing to work towards a better understanding of the breadth and complexity of the immune system—not just how it reacts to HIV and the virus’ mutations. For example, over the course of this research, we have discovered that some fragments of the immune system are stronger than others. We have also uncovered another component of our immune system that attacks HIV: natural killer cells.

These and other discoveries made through our research have the potential to help millions through the prevention of HIV and perhaps, one day, a cure. It could also have ramifications for research on how the immune system responds to other diseases, such as cancer and diabetes. Until the day we find a vaccine and perhaps even a cure, World AIDS Day will continue to remind us that the fight against HIV has not yet been won.

Through my work with academics in Brazil, I have witnessed an increasing awareness of the importance of computing in advancing scientific research in such areas as bioenergy, biodiversity, climate change, and plant physiology. In order to advance these fields, scientists need to deal with increasingly complex projects that require the expertise of a multidisciplinary team, and computing is a key element in this effort.

In light of this need, the Microsoft Research-FAPESP Institute launched the Portuguese translation of The Fourth Paradigm: Data-Intensive Scientific Discovery, a wide-ranging collection of essays on the process and promise of data-intensive science. An outgrowth of the thinking of late Microsoft researcher Jim Gray, The Fourth Paradigm sets out the parameters of twenty-first-century eScience.

The launch of the Portuguese edition took place on November 3, 2011, at FAPESP in São Paulo. Professor Carlos Henrique de Brito Cruz, FAPESP’s scientific director, opened the launch event, observing that “Science advances mostly through the development and application of new instruments. Computing power, the cloud, and other facilities constitute a big new instrument that allows researchers to obtain and analyze gigantic data sets in a way which was not possible a few years ago. The Fourth Paradigm deals with this fascinating window of opportunity for science and a Portuguese translation will contribute to the visibility of the authors’ ideas in Brazil.”

Professor Roberto Marcondes Cesar, Jr., who supervised the translation into Portuguese, then spoke about eScience in Brazil. “The Brazilian computer science community has been working together with domain scientists for decades in fields such as astronomy, geoscience, bioenergy, and medicine—to name but a few. Different expressive results addressing relevant problems for the country have been achieved and the Brazilian CS [computer science] researchers proceed to increase the collaboration results both in volume and quality. In this sense, the Portuguese translation of The Fourth Paradigm represents an important step in disseminating eScience methods and opportunities, both to attract CS researchers and students to the field and to draw the attention of domain scientists who may benefit from interdisciplinary research.”

These comments set the stage for a talk by Dan Fay, the director of Microsoft Research Connection’s Earth, Energy, and Environment activities, who said, in part: “For scientists, access to massive amounts of data can be a blessing and a curse—finding the significant nuggets of information that will lead to insights in the huge volumes of data is the problem. Big data is as much challenge as opportunity. When you have data sets as a large as a petabyte, that’s always going to be difficult to move around and analyze… The science of big data is as much about asking the right questions, so that scientists collect the right data, as it is trying to sift through data after the fact.”

Microsoft Research Connections is proud to partner with FAPESP in the pursuit of data-intensive research, as together we explore the use of computing technology to meet the social and economic needs in the Brazilian state of São Paulo. Oh, and this is how you say “fourth paradigm” in Portuguese: o quarto paradigma.

—Juliana Salles, Senior Research Program Manager, Microsoft Research Connections